Take This Darkness from My Soul
by lakota1954
Summary: This is a Coulson/Skye story that explores his thoughts and emotions after the events of Turn, Turn, Turn. Skye is at odds with her feelings toward Ward as well, but together they lead the team in its efforts to fight evil. All team members are involved in this story.
1. Chapter 1

Take This Darkness from My Soul

**A/N Story takes place right after the events in Turn, Turn, Turn. Spoilers for that ep. Thanks to Don McLean for the title. If you haven't listened to his song "Crossroads" maybe try to, it's Coulson's Song in my head.**

He sat on the edge of his bed, still dressed in his suit without the jacket and tie because he was exhausted and hoping against hope that he might find himself falling asleep. The loyal S.H.I.E.L.D. agents who were still alive had worked tirelessly to repair the bus over the last hours, and even though he had ordered the rest of his team to bed, he felt that he should help in any way he could. So he had been sweeping up glass, taking destroyed items off the bus and making sure that the items Jemma, Fitz and Skye had requested made it onboard. They were taking as many supplies as they could since they had no way of knowing when or even if they would get the chance to come back.

Now, it was 2 a.m. and everything that could be done had. May had gotten a few hours' sleep and now she was in the cockpit. They were heading to the Fridge, because Agent Hand had failed to check in with Coulson as she had promised. He sighed in frustration, knowing and yet not knowing if this was the right course of action. It could be another trap, but he knew he had to make sure that Garrett was locked up and that Ward was safe. For once in his life, Coulson was doubting his own leadership, his own decision-making skills. He knew the effects of lack of sleep on the human body and he suspected that was the major cause of his mental condition, but a nagging voice in his subconscious kept repeating May's words about them needing someone to reprogram his brain if it was necessary. Those words had sent an icy path down his spine. He knew that he shouldn't, but he was well aware that he was beginning to doubt his own loyalty to S.H.I.E.L.D. He was beginning to worry that even _he_ was not in control of whatever was in _his_ head.

He got up and began another walk around the plane. Seeing things in order helped to calm him, and even though there were unopened boxes all over and some signs of the damage they had sustained, it was still familiar and offered as much safety as his new world could. He immediately picked up on the light from under Skye's door and his feet seemed to move unbidden toward it. As he got closer the door unexpectedly opened and he came face to face with the young hacker. She took one look at his appearance and stance and spoke.

"AC, come sit down." Skye took hold of his arm and led him to her bunk where he sat mutely. She reached behind her and shut the door. Whatever was going on here, she wanted him to have his privacy. She perched beside him on the bed, noticing that he clutched the phone that Agent Hand had given him tightly.

"Did Agent Hand call?" He shook his head and looked at the phone.

"No. But, she should have by now. I've instructed May to set a course for the Fridge." He looked expectantly at her and then down at his lap. The terrible toll of leadership weighed heavily on his shoulders. "Skye," he began, "I just… I just don't know anymore. I wanted to check with someone, to share… something." He looked lost for a moment and Skye just reached over and laid her hand on his knee encouraging him to continue. He looked at her and she saw the loneliness and confusion on his face.

"There… there's just no one." He continued shaking his head and she finally understood.

"May betrayed you." She said softly and winced as he flinched noticeably. "AC, I can't replace her, but I can listen. Whatever it is, you have my promise, for whatever it's worth to you, that our conversation will go no further than this room."

Coulson heard her and he knew she meant it, but he was too emotional and lost to take a lot of comfort in the words. He wanted more than anything to just shut off his thoughts and sleep. Sleep with no nightmares and no concerns. But, he knew that wasn't going to happen and now he had to draw upon every last reserve he had to try to help himself get through this. He reached out and put his free hand on hers where it lay on his knee. Surprisingly, he felt a connection that he hadn't felt for another human being in a long time.

"I'm sorry." He told Skye sincerely. She looked surprised.

"What are you sorry for?" She still hadn't grasped his meaning.

"Ward. Ward was on that plane and now we don't know where it is." He spoke softly trying to spare her feelings. "I know you had feelings for him, Skye. Now, I've sent him off to god knows what fate. I shouldn't have let him go." He looked away.

Skye didn't remove her hand. Instead, she reached with her other hand and turned Coulson's face toward hers. She made sure that he was looking at her before she spoke.

"Ward volunteered for that mission, AC. It was _his_ choice. You let him have that because you wanted to give him closure after Garrett's betrayal. You didn't know that you were putting him in danger. We don't even know yet that there is a problem. Maybe the plane had engine trouble, maybe Hand just got super busy and forgot to check in. I doubt that, but the point is that we don't know. You made the right decision to go check on them and get the answers, when you could have just disbanded this team altogether. Think about it. Jemma, Fitz and I all have skills that could be used in the private sector. But, you stayed on as team leader because we wanted you to. Because we all share the desire to continue the fight against Hydra no matter the odds. And you wouldn't let us do it alone even after everyone betrayed you." She grabbed the front of his shirt in a bold move to make sure she had his attention.

"Whatever was done to you in T.A.H.I.T.I. is not changing _who_ you are!"

Coulson blinked and stared at her intense face. He had needed this… this confirmation of who he was. The events of the months since he'd died had worn away at him until he felt like an exposed nerve with nothing to mute the raw emotions that chased him night and day. But, this girl was like a salve that cooled and softened the pain. He managed a small grin and she got up and, to his surprise, took off his shoes. Without a word she pushed at him to lay down on the bunk and pulled the blanket over him.

"I won't sleep." He muttered the truth, but she just smiled. Curling up next to him, she pulled his arm around herself and softly spoke…

"Then just rest."

To be continued.


	2. Chapter 2

Take This Darkness from My Soul

Chapter 2.

Skye listened to the comforting drone of the Bus's engines as she lay cuddled in her bunk with Coulson. At one time she would have felt embarrassed at this closeness because he was, in fact, her boss. But, the months together on this plane had changed them. The mutual bond they had forged literally in blood was strong and undeniable. Whatever was coursing through her veins was doing the same in his. That was just the physical part, but she knew the psychological effects were much more binding. They had both been subjected to something that forever made them different. Made them outcasts in some ways, even though only a few people were aware of that. She realized that having him close was not only nice, but needed as well. Here, with his arm draped over her waist, she felt safe and loved. Others might view them from afar as a very odd couple, but she didn't really care. To her, the bond of soul to soul was far greater than any physical appearance could ever be. Her hand was sliding up and down through the fine hair on his arm as she thought, and he realized that she was, like him, still awake.

"What's bothering you?" He said softly as he rolled onto his back. Missing his touch, Skye turned also and laid her head on his chest.

"I… I did something stupid." She replied.

"No, not you." Coulson teased, and it made her smile. She hesitated because she wasn't completely sure he would understand.

"I'm listening." He said. "I can't guarantee I'll be much help, but I can listen." Skye found it easier to talk to his belly than to watch his face, so she kept her head on his chest.

"I kissed Ward." She waited for a response, but it didn't come. He was giving her the time to sort out things for herself. She sighed and continued.

"All my life I've been attracted to a certain kind of man. The pretty ones, the bad boys. The ones who I knew I could easily get, but also the ones who had so many problems that I was never more than a physical comfort to. And, I let that… that _pattern_ lead me again with Ward. But, now that I've had time to think, I really am ready to move past that. I think, I _know, _that relationships are based on more than just physical needs. At least the ones that last are. People that stay together share much more. They share trust and common interests. They have similar senses of humor and their ideologies match." She sighed as she came to the realization that this was the truest difference between Ward and her. She sat up a little and was able to look her AC in the eye.

"Ward killed a man in cold blood because of me." She said. "I can't justify that to myself. I can't live with that on my conscience." She met Coulson's eyes. "You would have never done that for me, because that's not in you."

"It wouldn't mean that I didn't love you." Coulson said sincerely. Skye reached up and put her fingers on his mouth to stop him from saying anything else.

"I know." She said firmly. "But the point I'm making is exactly that. You would not give up your integrity for someone else. And that's a very honorable and honest thing. Girls," she continued, "want boys who will change themselves to make a girl happy. Women, however, fall in love with men because of who they are, not who they can change them to be. Is this making any sense?"

Coulson smiled as she removed her fingers so he could respond. "It makes a lot of sense." He said firmly. She smiled and snuggled up to him again.

"Your turn." She told him. He sighed, but then spoke.

"When I was patching up May she told me some things. She told me that she had picked this team for Fury, that she was here to watch me, and that they were here to reprogram me or put me down if needed if I went awry." Skye sat up in shock.

"Put you down?" She said with fire in her eyes. "What the hell, AC? You're not a damn dog!"

He appreciated her anger because it matched his own. "Now you see how much May's betrayal hurt me. I don't know how to act now. I can't just be myself, because I don't know if I'll say or do something that she may see as wrong. I… I can't even be tired, or sick or hurt." He looked at Skye and she saw the fear in his eyes. "There is no way anyone will ever reprogram me, Skye. I will kill myself before that ever happens."

Skye took his words in and tried to process them quickly. He needed her to say the right things at this moment. She reached out and placed her hands on either side of his face.

"Okay, listen to me now. You are fine. I don't know why she said those things to you, but I didn't know you before, okay? From the time I first met you, your sanity has never been an issue in any way. And if it is, I will let you know. But," she continued, "you can't try to walk around being some sort of perfect robot. You have feelings and thoughts that are not in any way in need of "reprogramming." Skye winced at the words May had used. "Just be yourself, AC. What is inside here," she touched his chest over his heart, "is true and honest. You don't have to worry about that."

His eyes filled with tears for a moment at the relief he felt. Here was someone he could trust even as his world threatened to crumble. He felt safe and comforted.

Just then alarms began sounding in the cabin and throughout the plane. May's voice came on the intercom. "We've got company," she said, "two aircraft coming in starboard." Coulson was pulling on his shoes as he and Skye exited the bunk and headed toward the cockpit. They got a look from Fitz and Simmons who were coming out of their bunks, but simply didn't care.

"Fitz, get the guns up and running." Coulson said. "Skye, see if you can tell if they are preparing weapons to fire on us. I don't want to start shooting at them until we know if they are friendlies."

May looked up as Coulson entered the cockpit. He was dressed in wrinkled pants and his shirt was slightly unbuttoned. She wondered what he had been doing, but decided against asking.

"What do we got, May?" He asked.

"I think they're S.H.I.E.L.D." she replied. "No way to tell if they are friendly though. I can't raise anyone."

"Go to the emergency channel." Coulson ordered as he picked up the mike. "Attention S.H.I.E.L.D. aircraft this is 616. We are NOT compromised. I repeat, we are NOT compromised. We are on orders to meet Agent Victoria Hand at the Fridge. Do you copy?"

May stiffened as the planes came nearer. Coulson could tell that she was fighting a desire to overrule his command and take evasive action.

"Coulson, we might have to shoot them down." She warned.

"Not until we know they are threats." He said firmly. She got angry.

"One missile from them and we could all be dead!" She practically shouted at him. "Are you willing to sacrifice us all?" Coulson's jaw was set as he replied grimly.

"If it means that we don't kill innocent people needlessly, then yes."

Skye took that moment to burst into the cockpit. "They are friendly!" She practically shouted. "Their radios are out, but I was able to get through on the computers. They are loyalists whose orders are to report to the Hub. Their weapons aren't even working."

They watched as the two planes crossed ahead of them on their journey. One of the pilots dipped a wing at them as they passed. May shook her head. She was not satisfied.

"They could have been lying, Phil." She said firmly. Coulson took in her words and replied without hesitation.

"Yeah, there's a lot of that going around. And, May…" she looked up to see his dark eyes glaring at her, "don't call me Phil."

He walked purposely out of the cockpit with Skye following. She quickly caught up to him in the hall where they were alone. Taking his arm, she stopped him and leaned up to give him a quick kiss on the cheek.

"Now that was my AC!" She smiled proudly at him. He flushed a little, but was very appreciative. He'd followed his instincts and saved some innocent lives. He and Skye agreed to go change and shower. They would meet up with the rest of the team later to discuss different plans depending on what they found at the Fridge. He absently patted his pocket where the phone Hand had given him was. Things were not looking good, but he felt a fresh surge of confidence after his conversation with Skye. He realized that staying true to who he was would be key in the months to come.

To be continued.


	3. Chapter 3

Take This Darkness from My Soul

**A/N More on the rest of the team in this chapter.**

Chapter 3.

Skye finished cleaning up and ventured into the lounge. May was sitting at the bar, and unless Skye was mistaken, she had been crying. When the older agent saw her approach she ran a quick hand over her face and stiffened. Skye sat down next to her.

"You okay?" she said gently. They had all been through so much lately and Skye realized that without Ward and Coulson, May really had no one to talk to. However she felt about May's actions regarding her AC, Skye did not lose her sense of compassion for others. If May needed someone, she would try to be there for her.

May glanced at her and Skye saw the stark sense of defeat on her face, and sympathy tugged at her heart.

"I guess you hate me too." May said grimly. Skye's brow wrinkled in concern.

"No, of course I don't hate you, May." She said. "And neither does Coulson. He's just very hurt and confused right now. Surely you can understand that." May's shoulders slumped.

"We go way back you know." She told Skye. "I can't even count the number of times we have supported each other, watched each other's backs. When he…..died, I was devastated. I guess he told you what I confessed to him?" Skye remained silent. This was the line she had drawn when it came to Coulson. Nothing he told her would be repeated unless she had his permission.

May shrugged and went on. "I picked out this team for Fury. It included people who could reprogram him, or….. take him out if necessary." Skye gritted her teeth. This statement still lacked all humanity in her reasoning.

"You would kill your friend if he didn't act the way you thought was appropriate?" She asked, trying to keep any accusation out of her tone. May looked surprised.

"No!" She exclaimed. "I didn't mean it that way. I meant that if he began to suffer because of the T.A.H.I.T.I. treatment, that I would help him. He's been through so much, Skye. I couldn't bear to see him suffer anymore. Fury didn't know. That's why I wanted to be on this team. To make sure Coulson would never again suffer like he did."

Skye believed her. She felt the same way too, although her approach was different. She wanted to get him away if something went askew. She wanted to try to remove him from this situation, but in a different way. She sighed.

"Then I think we are both on the same page, May. But, you need to understand that what you said hurt him badly and it may take a while for him to recover from that. After talking with you, I think I can try to help if you give me permission to tell him what we just talked about."

May's eyes lit up. "You would do that? Yes, please, tell him. I never meant to hurt him."

Skye nodded. "It'll be a good start, May. There have been enough misconceptions and lies on this bus as it is…." Just then, Coulson came in the room followed by Fitz and Simmons. Everyone seemed to know to sit down and they all stared grimly at each other. You could have cut the tension with a knife.

Coulson cleared his throat and then said, "I think it's time for truth or dare without the dare. If we can't get all our secrets out, then this team is finished. The lies are tearing us apart better than Hydra ever could." He shook his head. "I know S.H.I.E.L.D. has indoctrinated us with the need to know level system, but the agency has been taken down. I'm not sure anymore that that system can be effective when we are on our own, and we depend on only each other. I think it's time we be open and honest with each other to get the job done. We need to have complete trust in each other, and that can't happen when we all hold secrets that effect the members of this team. So, with Skye's permission, I'd like to start by telling you my own." He looked at Skye, prepared to follow whatever her decision was. She smiled at him.

"I think it's time, AC." She agreed.

"Okay." Coulson looked around at the group. "The thing that brought me back to life, the ingredient in GH 325, was taken from an alien. This is what I saw when we broke into the bunker behind a door marked T.A.H.I.T.I. Resting in a tube of fluid was a dead, blue alien with tubes that were extracting the fluid. When I discovered it, I was in shock at first. Then I realized that you were going to give it to Skye and I panicked." He looked at Jemma. "That's why I tried to stop you. That's why I didn't want you to know what it was. I was afraid that your knowing would make you more vulnerable to the Clairvoyant."

Jemma's face reddened. "You were trying to protect me." She sighed. "I wanted to go to the Hub because I had taken a blood sample from Skye and I wanted to get it analyzed." She slammed her fist down on her knee. "Bollocks! That info is on a computer at the Hub now. Anyone could possibly see it."

Skye figured it was her turn. She cleared her throat and announced her confession about being an 0-8-4.

"Do you have powers?" Fitz asked excitedly.

"Not so far." Skye shrugged her shoulders. May opted to go next and explained about reporting to Fury.

"But, that's all over." She said tersely as she looked at Phil. "My loyalty is to only those in this plane right now. And to Ward of course."

Coulson seemed to have a strange look on his face. He spoke to the rest of them.

"I know this is hard for you, but it has to be said. Ward…. uh Ward is… off. I don't know why he insisted on going to the Fridge with Hand. I just find it disconcerting that he so completely changed his feelings about the man he looked up to. I was stung by what Garrett did as well, but it's very hard to abruptly make your feelings take an about face like that. We definitely need to talk to him."

The others took this in without comment. Ward was not here to defend himself, so they followed Coulson's lead and gave him the benefit of the doubt until they could question him in person.

"Sir, I think there is one more issue." Fitz's face reddened as he spoke up.

"What is it, Fitz?" Skye asked.

"Well, it's about protocol." Fitz replied, determined to get through this. "Jemma and I saw you and Agent Coulson coming out of _your_ bunk this morning, Skye. I… I mean is having a relationship on the Bus okay now?"

Coulson just burst out laughing and Skye smiled. The others looked on in shock.

"Fitz, as long as it doesn't hinder our work, you can sleep wherever you want. To be completely honest, I've always thought that particular protocol was a little too intrusive. We all need some comfort at times." He said as he looked at Skye and smiled.

May smiled too, but it was a sad one. She could only hope that her fractured relationship with Coulson would gradually be repaired in time, but she also realized that he and Skye had a bond like no other couple on Earth that she knew of. Honestly, she was happy for them.

The team decided to break up for the next few hours. Fitzsimmons wanted to unpack all their replacement equipment. May wanted to try to locate friendlies over the airwaves. Skye still had to repair onboard electronics. Left with no paperwork, Coulson decided to enjoy mindless cleaning up and repairing the inside of the plane as best he could. He was actually quite handy after years of practice living on his own.

Everyone seemed to have a new energy and focus now that the major secrets were out. They were still raw from the last hours, but hope was peeking out from around the corners at last.

To be continued.


	4. Chapter 4

Take This Darkness from My Soul

**A/N This chapter takes us up to the preview for "Providence." I'll start updating after that ep.**

Chapter 4.

Skye wasn't really asleep, but she was comfortable drifting when she was startled by the soft knock on her door. Opening it she was surprised to see a very rumpled Coulson standing there, wearing a tee shirt and sleep pants and with a look of fear on his face. She silently stepped back and let him in knowing he wouldn't come here if it wasn't important. She sat back down on the bed, but Coulson stood trembling for a moment before he sank to his knees on the carpet.

"AC, what…?" Skye began, but a tremendous sob escaped him then and instinctually she drew his head onto her lap and began to rub his neck and shoulders. Leaning down, she placed soft kisses on the top of his head and held on while he sobbed wretchedly.

After a few minutes, he became more still and his arms circled her waist as he held onto her tightly. She knew something big had happened to cause him to have a total meltdown like this, and she patiently waited him out knowing comfort was what he needed most now. Finally he spoke in a broken, almost childlike voice.

"I am so sorry, Skye." She rolled her eyes internally at the statement, knowing immediately that whatever had happened might affect her, but sincerely believing her AC was not at fault. She reached behind her and pulled some tissues from a box and gave them to him. With a little help, he managed to stand and then sit next to her as she kept his hand in a tight grip.

"What happened?" She asked softly. He swallowed and his eyes filled with unshed tears.

"I couldn't wait any longer, so I called Agent Hand." He stopped and wiped his eyes. He couldn't look at her when he said the rest. "Someone else answered, and I knew that she was probably dead, Skye." Skye was confused.

"Maybe she was just busy and someone else answered her phone?" She questioned, but Coulson shook his head.

"They…. they didn't just say hello, Skye." He looked at her through red eyes. "They said, _**Hail Hydra**_!"

Skye stiffened and held onto his hand more tightly. He ducked his head and spoke softly.

"And it gets worse." He took a deep breath and faced her. "It was Ward. I recognized his voice. I…I was worried when he shot the fake Clairvoyant, and when he asked to go along to lock up Garret, I had doubts as well. But, I thought that I should give him a chance at closure. Now… well, I guess I've gotten three more loyal S.H.I.E.L.D. agents killed."

Skye was stunned. Ward? As she processed the information, she realized that maybe they all should have seen this coming. Ward wanted approval and acceptance, and he was ready to get it any way he could. Garrett, she realized, had turned him with his father-like companionship. All the while Coulson had been trying to get Ward to realize the importance of moral strength and integrity, Garrett had been so accepting of everything Ward did, right or wrong. He had encouraged the young man to take what made him feel good and powerful regardless of where it came from. Ward had learned to take his self-worth from pleasing the older agent, and from being more powerful than others. She actually felt sorry for him slightly because of how empty he must be inside to betray them all like that. She scooted over on the bed and hugged her AC for all she was worth. His tears, his fear, his actual guilt over the latest events, made her realize how different he and Ward were. Coulson found no joy in power over helpless individuals, he followed a moral compass that was the most important thing to him. And, she realized, if it became possible, he would give Ward a second chance. She understood too that he was fallible and human. Sometimes even he needed support. Skye's hand came up to cup his jaw as she leaned back to look him in the eye.

"It's going to be okay." She said simply as she leaned in and kissed him deeply. It wasn't really a sexual kiss, at least not this time. It was a kiss of comfort and trust. She wanted him to know that for now and forever, she was his. His trusted companion, his sounding board, and his comfort if and when he ever chose to do that with her.

Coulson felt her soft lips on his and unconsciously surrendered for a moment. His mind was tangled with lies and betrayal, but this woman was offering something pure and simple. He reveled in the feeling and for once didn't over-think it at all. It ended too soon, but it had served its purpose. He knew he had a mission again. He was reminded that not only Skye, but Fitz, Jemma and May needed him as well. Skye pulled back and saw the spark in his eyes.

"What's the plan, boss?" She asked him.

"Well, we're not going to the Fridge. For all we know it's been compromised and is a trap." He rubbed the back of his neck. "But, I think I know a place where we could be safe for a while." Coulson stood and held Skye's hand. To her surprise, he pulled it to his mouth and kissed the back like a true gentleman. She actually blushed. Old-fashioned may be corny, but it still worked as she felt her heart speed up a bit.

"Thanks, Skye." He said softly. "I have to go tell May the course change. Will you tell the others to start getting ready? They'll need their cold weather gear. It's below freezing where we're headed." Skye nodded, excited for the new adventure. Her heart caught for a second when she remembered Ward, but he had made his choice, and she hers.

They were all dressed snugly in sweaters, coats, hats and gloves. Coulson led the way through the snow as they dodged around the icy trees and rocks. May kept glancing at him as they went. She was back to being a bit suspicious since she had no idea where he was taking them. It had crossed her mind that he had finally snapped and they were going to be lost in a frozen wilderness soon. Skye was the only one who was energetically following their leader with no complaints. May sometimes wished she was that girl again, capable of that kind of trust.

Coulson finally stopped at what looked like a large cliff wall. He began to go from rock to rock, brushing off the snow, looking for something. May rolled her eyes and finally spoke.

"Are you looking for a specific rock?" She asked. "Because they all look pretty much the same to me…."

"Found it!" He interrupted her. Pushing against something only he saw on the rock, he stood back and looked toward the cliff wall. To everyone's amazement, the wall began to move. It turned out to be a large door that slid aside to reveal a tunnel passageway. Coulson didn't hesitate to step forward and motioned everyone to join him in the tunnel. Once they had all entered, he pushed a button on the inside and the wall slowly reversed until it had closed them in.

"Jesus, Coulson, I hope you know what you're doing." May said suspiciously. He looked at her with contempt.

"I'm trying to find a place for us to be safe, if that's alright with you." Coulson turned to the others. "I discovered this place years ago when I had parachuted out over this area. My ankle got broken in the drop and I had resigned myself to a certain death. I passed out at one point, and when I woke up, I was inside here. Hopefully, they are still friendly." He shook his head looking undecided for a moment, but that ended when Skye took his hand and began to walk them forward. He smiled down at her, appreciating the much-needed vote of confidence.

"It was a good plan, AC. Sometimes taking a chance does pay off."

He surprised himself then by leaning down and kissing her softly on the lips right there in front of the whole team.

"I know." He told her as they began the walk into the next adventure.

TBC


	5. Chapter 5

Take This Darkness from My Soul

**A/N This story is definitely AU after the events of Providence, but my Coulson/Skye pairing continues on. I am not putting down any other pairing, I just think there's an emotional connection between these two that stems from their beliefs and backgrounds that just isn't there with the canon pairings. But, I recognize that others see that in the canon pairings and I appreciate their views as well. We can all agree that we love this show!**

Chapter 5.

Skye and the others had enjoyed showers and changes of clothing. Surprisingly, Providence provided jeans and shirts in many styles and sizes so they all found something appropriate to wear. She wandered the many rooms in the secret base looking for her AC. He had very nearly broken when she had told him they were agents of nothing, and she realized how much that must have hurt him. She had silently cursed herself for having such a sarcastic mouth the minute the words had come out, and she saw his expression. She made her way into the cafeteria which, at first glance, seemed empty. Then she saw him in a corner booth, wearing clean clothes that weren't a suit, and resting his head on an elbow. He didn't see or hear her. She could tell he was miles away, inside his own head. Approaching carefully, she slid into the booth next to him. He finally stirred and gave her a small smile, his eyes still far away.

"They're going to have dinner in a while. Turns out Koenig is a pretty good cook. Are you hungry?" She asked him. He blinked and seemed to come back to the present.

"Not really." He answered softly. "But you should go eat."

Skye sighed and then spoke quickly. "God, AC, I am so sorry for that inappropriate comment about us being agents of nothing. It had to be hurtful since you've given your life to S.H.I.E.L.D. I… I've never had anything to really believe in during my life, and I am so sorry." Coulson seemed to relax a little as he looked at her with obvious affection. He shook his head.

"It's not your fault that this is all happening…." He hesitated, but then continued. "You know all my life I've been the problem solver, the guy in charge." He looked at Skye and seemed to make a decision. "I was six when my father was killed. My mom….well, she really never had the capacity to be a mom. She was raised in a very dysfunctional family, and just never had the tools to deal with her own child. My father's death broke her. She turned to drugs and alcohol to help her through it, and I was well, not a part of her survival methods. I think she pretty much resented me for forcing her to be responsible, to be a parent. So, I got passed around to other relatives for a bit, but that got to be a real inconvenience to them. I started living back with her full time when I was eleven. By then, I had something to offer her. I paid the bills, cleaned house, made sure there was food in the pantry." He smiled ruefully at the memories, and then continued.

"She and I were like ships in the night, passing each other occasionally, but never really noticing. I learned very young that what I could _do_ for people was much more important than what I _was_." Skye's eyes had begun to tear at his story, but she refused to let them fall. He didn't want pity, he wanted understanding. Without a second thought, she put her arms around him and hugged him tightly even when she felt him stiffen. She needed to help him, to get through to him somehow.

"AC, you must know this. Whatever happens with S.H.I.E.L.D. or this team, I love you for what _you _are. Right now, I'd be okay with just going away, making new identities and being on the run for the rest of our lives. It wouldn't matter what we did as long as I was with you. What you are is kind, gentle, and honest." She smiled, "And a little hot!" He finally looked her straight in the eyes and grinned.

"Just a little?" He teased. She sat back and studied him.

"Well, before I can upgrade you, I have to see what's under the hood." She said cheekily and laughed when he turned red. "Come eat with me now?" He took her hand and they slid out of the booth and joined the others who had been gathering at some tables in the front of the cafeteria.

Eric Koenig was true to his word and had cooked a meal of baked chicken, rice pilaf, and buttered asparagus that was delicious. As they sat around the table eating and talking, Coulson was finally able to relax and even ate a small amount. It helped that Skye kept her hand under the table, discretely placed on his thigh. The physical closeness was something he was very unused to. He had grown up without any physical or verbal love, and had only experienced it in the few times he had been with a girlfriend. But, his fear of intimacy always drove them off before they could really get to know him. Skye was so different from any other woman he had been attracted to. She did not judge him when he tended to withdraw from her. Instead, she purposely came after him, not letting him get away to his safe but lonely place. She even understood why he retreated there, and could empathize with why he did it. It was hard, but he began to let himself have some hope for the future.

And as he looked around the table, he felt lucky to be in the presence of these people. Jemma was glowing as she told another funny story about Fitz from their academy days. Fitz was giving her a loving look, whether it was romantic love or not, Coulson still didn't know. May participated politely, but she was sending sad looks his way. He decided that this was something he needed to address in private with her.

"Well," Agent Triplett announced, "since I'm the new guy, I'll take K.P. duty tonight." He stood and started to collect the empty dishes as the others gave him grateful looks. Everyone started to wander toward the bedroom area of the base. Coulson pulled Skye aside.

"I've got to make something right." He said to her as he looked pointedly at May. He squeezed her hand. She nodded in understanding and gave him a brief kiss.

"I'm glad you're going to do that, AC. You've been friends too long to let it all go south."

Coulson rushed to catch up with May and Skye watched as he led her to a small sofa in the hallway. Then she walked toward the bedrooms, confident that she would see him again tonight. Hopefully!

"I wanted to tell you that I'm sorry for acting like an ass, May." Coulson began as soon as they sat. He looked at her, but did not make any excuses for his actions. That was not his way. He had let her betrayal turn into much more than it was, and had refused to see her side of the issue. For that he was sorry. He wanted to try to repair things with her, but knew it was her decision. May watched his eyes, trying to read him like she always had. She didn't see any deception or falsity in them. She sighed.

"I was wrong to not see your true intentions." Coulson continued. May reached out and gently touched his face for a moment.

"And I was wrong to doubt your judgment, Phil. Whatever Fury had done to you has not changed you. At least not for the worse. You are more forgiving and kind now. At first it scared me. To think… to think that something had taken over your mind. But, now I realize that whatever they did only enhanced qualities that you already had. So, I'm sorry too. Maybe we can get past this?" She smiled tentatively at him. He felt a wave of warmth spread through him as he realized that maybe he could salvage his old friendship.

"I would like that very much." He said firmly as he looked into her eyes. And to his astonishment, May actually leaned forward and drew him into a friendly hug. For Phil Coulson, being hugged twice in one day was a true first, and he enjoyed the sentiment immensely.

The two agents drew apart and began to head down the hall toward the bedrooms. Coulson really wanted to join Skye, but all the doors were closed and he didn't know which was hers.

"I think you may want that one." May said dryly as she indicated a door. Someone had pulled the yellow sticker off the room's air conditioner and stuck it on the door. Coulson smiled as he proceeded to open the unlocked door that bore his initials.

TBC


	6. Chapter 6

Take This Darkness from My Soul

Disclaimer: Just playing with Joss's toys for fun, not money.

**A/N This chapter rated M.**

Chapter 6.

Coulson stood at Skye's bedroom door. Sighing, he peeled the yellow sticker off and took stock of his thoughts and feelings. The feelings were _oh, hell yes_ without reserve, but of course, the thoughts held him back as usual. He actually couldn't remember a time in his life that he had acted on feelings without regard to all the consequences his brain threw at him. He was exceptionally good at talking himself out of anything that might provide comfort. His past had taught him that comfort was fleeting, and that to have any sort of stability in life one must eschew comfort and embrace logical thought. He began to tick off the logic in his head_. One, I'm a lot older than her. Two, she's still somewhat under my command. Three, perhaps the biggest obstacle, I'm supposed to be leading these people, not flaunting my sexual exploits in front of them._

For once, instead of stopping right then and there and walking off, Coulson remained where he was, head full of more thoughts. He remembered his outburst outside just a few hours ago. The looks on his team's faces were very clear. They thought he'd lost his marbles. He actually stood remembering his psyche classes at the academy. Wasn't there something about the very human need for physical and emotional support to make one stable? Did he lose it out there because for over a year he hadn't had any of that support? Sometimes he felt like his brain had turned on him. When he woke from horrible nightmares, when he felt so disconnected from the others, when he couldn't trust himself. He did desperately want someone to talk things out with, to not always have to be alone when making the hard choices. He looked down at his hand on the doorknob and was amazed to be able to focus on the flesh itself. Instead of just an object used to complete a task, he let himself see the skin and hair and he flexed his fingers to feel the movement. This is what makes me a human, he thought to himself. And even though touch was not something he experienced much in his life, he realized at that moment that he needed it. It made him feel good. It made him feel human. Squaring his shoulders and taking a deep breath, he let himself into Skye's bedroom.

"Skye?" He whispered because it was pretty dark and he didn't want to wake her. She was definitely not asleep. She stepped from behind a dresser and he gasped. She was very, very naked!

"Like what you see?" She teased as she approached him, stopping a few feet away. Coulson had unconsciously flattened himself against the door.

"I…. well, I thought we were going to talk." He squeaked, and she laughed. She took a big step forward and began to take his tie off. Smiling, she assured him that they would talk later. He was so astounded at her boldness that he let her unbutton and remove his shirt. He felt a twinge of regret as she stepped away and looked him over.

"I know, it's really ugly." He mumbled. "There's one on the back too." She frowned and he felt the need to explain. "Just giving you full disclosure. You've got a right to know my accident history after all… you know, since you wanted to see what's under the hood."

Skye ran her hands up and down on his upper arms. "Where did you get these?" She asked about the muscles that had been hidden under his shirt. "I've never seen you work out."

He grinned shyly. "I guess they are after market." She smiled and then his world went haywire when she finished undressing him. Her hands seemed to be everywhere at once and he just let himself drown in her lazy caresses. Thoughts left his head and were replaced by feelings. He made the effort to return the favors, but she would have none of it. She truly meant for this to be his time.

Moving them to the bed, she had him lay down and straddled his hips. He hadn't had sex in so long he was afraid that once she touched him it would be all over. But, Skye was patient and she kissed and rubbed and nipped at him until he thought he would explode. He felt her reach down and position him as she slowly lowered herself onto his shaft. Coulson felt that if there was a heaven then this would be it. He started to raise his hands to cup her breasts but she stopped him.

"Baby, I'm so close." She stammered out. His eyes fell shut as he let himself experience the feeling of her wrapped so intimately around him. He reached down between them and began to expertly thumb her, pushing up into her as she writhed in pleasure. When they both came, he just let himself feel his body, her body, and where they were joined. It was intense and calming at the same time. The buildup and release each as pleasurable as the other. They lay panting side by side until they fell asleep enjoying the softness of skin against skin.

The others looked up when Coulson and Skye came to the cafeteria for breakfast. Fitz watched in amusement as Coulson, who hadn't been eating much lately, filled his plate to overflowing with eggs, hash browns and bacon. He also got a large glass of orange juice.

"Nice to see your appetite back." May said dryly. She even had a knowing smile on her face. Coulson turned bright red and Skye felt sorry for him. He would be the one to get all the teasing in this relationship because of his age and, well, stereotypes. He still dug into his food with gusto, and she was relieved.

Koenig, who was oblivious to the situation, spoke up. "We've got to get your team vetted today, Agent Coulson."

"Vedded?" Coulson said around a mouthful of potatoes. Koenig nodded. "Fury left me with a state-of-the-art lie detector, and I can use it to make sure there are no Hydra spies on your team."

"Hydra spies?" Said Jemma, joining them. "We've been together a long time. I can assure you no one here is Hydra."

Even as they heard his words, the team couldn't help but look around the table at each other.

"Fury's orders." Said Koenig firmly. "Everyone except Agent Coulson."

Coulson felt lucky that he had finished most of his food before this part of the conversation. His appetite disappeared as he remembered his fight with May. She had told him that Fury was not the one who had replaced his memories, and now he shivered inwardly as he realized once again that he didn't know if he could trust himself.

"I want to be put in the lie detector." He said firmly, despite the pointed look from May. Koenig gave him a surprised look.

"Fury trusts you. There's no need."

"I have a need." Coulson said enigmatically as he looked around at the surprised group.

"Phil…" May started, but he gave her a soft look to let her know he wasn't still angry.

"I just….. need to know, May." He explained and she knew then that it had to happen.

Koenig shrugged. "Okay, then. Follow me." He led the group down the hall to another room. A large black chair dominated it. Koenig pointed to it. "Just sit in the chair Agent Coulson, and put on the headphone section." Coulson did as he was asked and settled into the chair as he felt the slight vibrations of electrical energy through the seat and back. Koenig cleared his throat.

"State your name and rank."

"Phillip Coulson, Agent of Shield." Coulson replied. The chair continued to vibrate. Koenig looked a little puzzled where he stood watching the results on a hidden screen, but he continued.

"Do you now, or have you ever worked for an agency called Hydra?" The team knew their leader well enough to be confident about his allegiance, but they were surprised when he turned pale and swallowed at the question.

"No, I have never worked for Hydra." Phil said clearly.

At this point, Koenig let out a mumbled whistle. The others fixed their gazes on him.

"It's just never done this before." He said as he moved the screen so that others could see it. The words on the screen were stark in their appearance and astonishing in their meaning. On the screen were the words:

**SUBJECT CANNOT BE READ. UNEXPLAINED INTERFERENCE PRESENT.**

tbc


	7. Chapter 7

Take This Darkness from My Soul

Disclaimer: I do not own or make money from these stories.

Chapter 7.

"What does it say?" Coulson asked from the chair. The others looked at the screen and then over at him. Before anyone could say anything, May took charge.

"Well, it's obviously not working." She said matter-of-factly. "Fitz, go change places with him."

Koenig was, fortunately, not the brightest bulb in the pack. He just sniffed and went about recalibrating his machine for the new subject. When Fitz changed places with Coulson, May motioned the older agent over to a corner of the room where she began talking to him in a very low voice. He looked upset at first, but then seemed to be agreeing with her. Skye watched as Fitz and Jemma finished their tests. After each finished, May talked quietly with them for a moment out of earshot. The hacker was mildly surprised when they left the room immediately after talking with May. Coulson stood in another area of the room, looking off in his own world again, and Skye was worried about him. She watched as Triplett passed his test. May confidently walked up to sit in the chair. Before Koenig could start the test, she asked him quietly about it.

"Does the chair indicate who is in it, or do you do that?"

"The chair knows just the basics of identification like male or female." Koenig replied. "I have to put in the subject's name. It doesn't record the voices, just analyzes their inflections to register deceit or honesty."

"So there's no record of who gave the test?" May asked.

"Wouldn't be needed here." Koenig replied. "I'm the one who always does it, and I type my name in first."

Concentrating hard, he spelled her name aloud to make sure he had it right. Just as she had answered the last question and gotten approval for her lanyard, Simmons burst in the room. She had ash on her face and smelled like smoke. Looking around in confusion she yelled at Koenig.

"Fitz was working on the fuel lines and started a fire on the plane!" She yelled. May had moved the plane to the hanger the night before. "Where are your fire extinguishers? We can't find them." She grabbed at Koenig and he put the screen he was using down. He looked torn and said to the others.

"We'll get back to this. Skye's the only one left." He rambled before leaving with Jemma and Trip.

May waited until they were all gone, save her, Coulson and Skye. Then she picked up the screen and gave it to Skye as she herself went to sit in the chair. Skye caught on quickly and recalibrated the machine, typing in the names.

"What is your name and rank?" She asked May.

"My name is Skye and I am an Agent of S.H.I.E.L.D." May said.

"Have you ever been affiliated with an agency named Hydra?" Skye inquired.

"No, never." May said succinctly. She waited for Skye to nod and then the three of them went to the machine that was printing out Skye's lanyard. Koenig chose that moment to return and when he saw a lanyard around Skye's neck he looked questioningly at them. Coulson finally spoke up.

"I figured that I would just do the test while we waited. No sense wasting any more time." Koenig actually looked a little suspicious for a moment, but then May was bombarding him with questions about her plane and the moment got lost. She left with him in tow, giving Skye a look while she nodded towards Coulson behind Koenig's back.

"What gives, AC? You didn't think I would pass?" She asked him. He looked at her and she saw his shoulders sag.

"I knew you wouldn't pass, Skye." He replied, but before she could react, he took her hands in his. "Look, there's only one reason that the machine couldn't read me. I know from Jemma's scans that they didn't put anything mechanical in my head or body, so that only leaves the alien blood." He looked into her eyes and said gravely, "If I wouldn't pass, then it stands to reason that you wouldn't either. And Koenig is not a bad guy. I didn't want to have to hurt him if he tried to lock you up."

Skye leaned her head back and closed her eyes and sighed. "I think I'm starting to not like being different so much."

Coulson stepped forward and gently tugged on her lanyard. "Get used to it, babe." He said as he leaned in and gave her a kiss. She opened her eyes and saw the depth of feeling he held for her in his eyes and it was comforting. At least one very special thing had come about because of that damn alien juice…

They found the others in the underground hangar. There was lots of shouting and fuss, but the tiny fire that they had started to lure Koenig from the lie detector chair had only been for show and nothing had really been damaged. The team began to load supplies as fast as they could and only stopped once to grab a quick dinner. They repainted the outside of the plane as best they could, and even though they had no dryer, the special aircraft paint that Koenig had given them, hardened to a high gloss metallic shine. Nothing with S.H.I.E.L.D. logos was left on the plane. They considered themselves still as agents, but knew that they couldn't get anything done from jail cells if they were caught. S.H.I.E.L.D. was now considered a terrorist group and they had to be careful. Plans were made to work out of Providence in complete anonymity, and Koenig assured them that Fury had planned for a long siege and supplies were plentiful. The group labored for two intense days, repairing and supplying the aircraft.

Somewhere toward the end of the second day, Coulson did a rather strange thing. Without thinking, he had bent down and picked up a large container with handles and flung it up to the waiting Triplett and Fitz aboard the plane. He didn't think anything of it until it landed at their feet and thumped heavily on the floor. Trip bent to get a handle and pulled. All three men were somewhat surprised when the box didn't move. Fitz had to take the other handle and together they slid the heavy box into its place without picking it up.

"How did he do that?" Trip asked Fitz when they were done. "I mean we couldn't pick it up between the two of us, and he just tossed it up here like it was nothing." Fitz just shrugged. Right now he was exhausted and felt relieved that they had finally finished the task. He looked forward to a hot bath and maybe a swim in the base's pool later.

Finally, they were done. Everyone enjoyed another great meal from the amazing Chef Koenig. Afterwards, they all agreed to meet at the pool for drinks and swimming, or really just floating because they all were sporting sore muscles.

"Look at you girl!" Jemma exclaimed as Skye walked into the pool area wearing a pink bikini that showed off her tanned skin perfectly. Skye walked over to them where they sat around a small table. Jemma hadn't gotten into the water yet, but Fitz was teasing her to get wet. He looked so cute in his red, white and blue trunks. He was by no means skinny, but he hadn't developed the muscle of say, Trip, who was seamlessly swimming laps in the oversize inground pool. May joined them wearing a two-piece suit that was flowered and had a swath of material bowed on her hip. It was so very feminine that it sort of shocked Skye at first.

"What?" May asked when she saw her expression. Skye smiled warmly at the woman.

"I guess I thought you'd have an official S.H.I.E.L.D. suit or something." Skye smiled.

"No, that'll be Coulson." She replied with a smirk.

"What'll be me?" They heard Coulson ask as he approached wearing simple navy trunks and a white tee shirt.

"Afraid you'll get too burned, Agent Coulson" Jemma reached over and tugged at the bottom of his shirt playfully, but he stepped back and looked upset.

"No, I…. well I don't want you to lose that lovely dinner you all just ate." He was trying way too hard to make a joke and no one laughed.

"Phil, if you want to keep that damn tee shirt on it's fine. But, don't do it to try to save our sensibilities. Those scars are a part of you, and as your friends, we accept them as we do you." May told him seriously. Phil stood stock still and seemed confused as to what to do or say about that. Skye walked over to him and whispered in his ear. He looked at her and the others could see the trust in his eyes. Skye reached down, grabbed the hem of his shirt and lifted it off in one swift move. Phil stood embarrassed and fought the desire to cross his arms over his chest.

"Wow. Where have you been hiding those arms, sir?" Jemma looked at him appreciatively.

"Oh, man, I'm still the scrawniest male here." Fitz added.

"Seriously? You've been working out all this time?" May commented. No one even mentioned the scar as his friends helped him feel at ease. Jemma even got up and ran her hand down his upper arm.

"I had to feel that for myself." She giggled. Skye gave her the evil eye.

"And, I think that's enough touching she said as she pulled her AC away from the group. They walked away toward the far, darker end of the pool. Coulson perched on the edge with Skye in the water between his knees.

"You know what this would be a great position for?" Skye said wickedly. Coulson looked up in surprise before he nudged her back and joined her in the water. It wasn't too deep and they could both stand with their heads above water. He pulled her in for a kiss and she reveled at how their skin felt it the soft, smooth water. Then, in one swift motion, he picked her up and tossed her, laughing delightedly as she came up sputtering and yelling at him.

"Oh now you gone and done it, boy. It's on!" She cried at him in mock anger.

"Gotta catch me first." He teased in that understated way with his eyes shining like she loved. He lowered into the water and started making powerful strokes away from her. Before she started to follow, Skye smiled to herself. It had taken the world to practically end, but she had finally found what she'd been looking for all along. Someone to love and protect her, and be at her side. Someone who treated her as an equal, and truly needed and loved her as much as she did him.

The end.


End file.
